Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 23.47 kDa 
• Atom Count: 1682 
• Residue Count: 192 
• Unique protein chains: 1

1T4E

Structure of Human MDM2 in complex with a Benzodiazepine Inhibitor

• DOI: 10.2210/pdb1T4E/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2004-04-29 Released: 2005-02-08 
• Deposition Author(s): Grasberger, B.L., Schubert, C., Koblish, H.K., Carver, T.E., Franks, C.F., Zhao, S.Y., Lu, T., LaFrance, L.V., Parks, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.276 
• R-Value Work: 0.239 

Literature

Discovery and cocrystal structure of benzodiazepinedione HDM2 antagonists that activate p53 in cells

Grasberger, B.L., Lu, T., Schubert, C., Parks, D.J., Carver, T.E., Koblish, H.K., Cummings, M.D., LaFrance, L.V.

(2005) J Med Chem 48: 909-912

• PubMed: 15715460 
• DOI: 10.1021/jm049137g
• Primary Citation of Related Structures:  
  1T4F, 1T4E


• PubMed Abstract: 
  

HDM2 binds to an alpha-helical transactivation domain of p53, inhibiting its tumor suppressive functions. A miniaturized thermal denaturation assay was used to screen chemical libraries, resulting in the discovery of a novel series of benzodiazepinedione antagonists of the HDM2-p53 interaction. The X-ray crystal structure of improved antagonists bound to HDM2 reveals their alpha-helix mimetic properties. These optimized molecules increase the transcription of p53 target genes and decrease proliferation of tumor cells expressing wild-type p53.

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Organizational Affiliation: 

Johnson & Johnson Pharmaceutical Research & Development L.L.C., 665 Stockton Drive, Exton, Pennsylvania 19341, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-protein ligase E3 Mdm2	A, B	96	Homo sapiens	Mutation(s): 0  Gene Names: MDM2 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
Find proteins for Q00987 (Homo sapiens) Explore Q00987  Go to UniProtKB:  Q00987
NIH Common Fund Data Resources
PHAROS  Q00987 GTEx  ENSG00000135679

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIZ	A, B	(4-CHLOROPHENYL)[3-(4-CHLOROPHENYL)-7-IODO-2,5-DIOXO-1,2,3,5-TETRAHYDRO-4H-1,4-BENZODIAZEPIN-4-YL]ACETIC ACID C23 H15 Cl2 I N2 O4 HQEQUYKKMMKSSX-PMACEKPBSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DIZ	IC50:  420   nM  BindingDB
DIZ	Kd:  80   nM  BindingDB
DIZ	Kd:  67   nM  BindingDB
DIZ	Kd :  80   nM  PDBBind
DIZ	IC50:  200   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.276 
• R-Value Work: 0.239 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 98.486	α = 90
b = 98.486	β = 90
c = 74.038	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
PROTEUM PLUS	data reduction
PROTEUM PLUS	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-04-29 
• Released Date: 2005-02-08 
Deposition Author(s): Grasberger, B.L., Schubert, C., Koblish, H.K., Carver, T.E., Franks, C.F., Zhao, S.Y., Lu, T., LaFrance, L.V., Parks, D.J.

Revision History 

• Version 1.0: 2005-02-08
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-11-16
  Changes: Atomic model
• Version 1.4: 2018-01-31
  Changes: Experimental preparation